Genome Annotation with Companion (Part 1) Companion, is an online pipeline that employs different software to annotate and compare an assembled sequence to a reference-annotated genome. The figure below illustrates the Companion pipeline, the software used and the expected output.

For this exercise, we will start with an assembled genome that is unannotated. We will obtain the assembled FASTA files from EuPathDB sites. Companion is housed at Sanger and can be accessed here: https://companion.sanger.ac.uk Each group will download one of the following genomes. The tinyURL links will initiate the download. Group 1 – Cryptosporidium baileyi TAMU-09Q1 – http://tinyurl.com/h7hwuo4 Group 2 – Cryptosporidium meleagridis UKMEL1 – http://tinyurl.com/goj2b2p Group 3 – Cryptosporidium hominis UKH1 – http://tinyurl.com/h97hf2w Group 4 – Plasmodium coatneyi Hackeri – http://tinyurl.com/z52bp33

Group 5 – Acanthamoeba palestinensis Reich (largest 3000 contigs) – http://tinyurl.com/j2rd9lq A note about downloading genomes and genomic sequences from EuPathDB sites: All genomes in EuPathDB sites are available for download form the “Data File” download section, which you can access from the Downloads menu in the gray tool bar.

Selecting the Data Files option takes you to the download directories where you can navigate to the genome and data type you are looking for.

To download specific contigs/scaffolds/chromosomes you can use a genomic sequence search and place the desired sequences into your basket.

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- Once you have downloaded your sequence file, go to the Companion site: https://companion.sanger.ac.uk - Click on the “Annotate your sequence” link.

-Follow the instructions as described on the Companion website: 1. Provide basic information about the job you are about to submit. This includes a job name, species prefix (usually the first letter of the genus and the first three letters of the species: Acanthamoeba palestinensis = Apal).

2. In step 2, choose the assembly file that you downloaded. 3. In step 3, indicate if you will be using RNAseq evidence to guide the annotation – in this exercise we will not use any RNAseq data. 4. In step 4, select the reference sequence you would like to use to transfer the annotation and to compare your sequence to. Typically you would like to use a reference that is closely related, so a phylogenetic tree might be useful to look at. Here are examples for Plasmodium and Cryptosporidium. There is only one reference for Acanthamoeba. http://tolweb.org/Plasmodium/68071 http://tolweb.org/Cryptosporidium/124803

5. In step 5, there a few more parameters you may want to examine. For the purpose of our exercise we will keep these at the default values.

6. Enter your email address to get an update when your job starts running and when it is complete. Next, click on the “I’m not a robot” captcha (Completely Automated Public Turing test to tell Computers and Humans Apart). Finally, click on the “Submit Job” link.